Table 3

Parameters used to assemble the individual and composite white spruce linkage maps.

Mapping parameters

Individual

maps

Composite map



Cross P

Cross D



♀80112

♂80109

♀77111

♂2388


Available markers a

600

671

521

508

1,578 b

Distorted markers c

10

12

15

19

33

Markers without segregation distortion

590

659

506

489

1545

Assigned markers

580

650

486

470

1,342

AFLP loci

256

289

-

-

470

SSR loci

9

10

-

-

12

Gene loci

ESTPs

22

23

20

20

33

SNPs

293

328

466

450

827 d

Total

315

351

486

470

860

Positioned marker loci (%)

549 (94.7)

570 (87.7)

471 (96.9)

454 (96.6)

1,301 (96.9)

AFLP loci

239

235

-

-

453

SSR loci

8

10

-

-

12

Gene loci

ESTPs

19

19

20

20

33

SNPs

283 e

306 f

451

434

803 g

Total

302

325

471

454

836

Major linkage groups (n > 10 markers)

12 (4 h)

12 (1 h)

12

12

12

Minor linkage groups (3 ≤ n ≤ 10 markers)

1

0

0

0

0

Unlinked markers

10

9

20

19

58

Map length GF, cM (Kosambi)

2,163.6

2,276.1

2,055.6

1,700.1

2,086.8

Average map density, cM (Kosambi)

3.9

4.0

4.4

3.7

1.6

Average size for major linkage groups, cM (Kosambi)

143.3

162.6

171.3

141.7

173.9


a For individual linkage maps, only markers segregating 1:1 or 1:1:1:1 were used.

b 256 markers were shared between the two crosses.

c Bonferroni correction: P ≤ 0.01/number of loci.

d 373 gene loci from Arborea PgLM0 SNP array, 339 from Arborea PgLM1 array, and 115 from Treenomix array.

e 215 gene loci from Arborea PgLM0 SNP array, and 68 from Treenomix array.

f 239 gene loci from Arborea PgLM0 SNP array, and 67 from Treenomix array.

g 370 gene loci from Arborea PgLM0 SNP array, 325 from Arborea PgLM1 array, and 108 from Treenomix array.

h Number of linkage groups composed of 2 subgroups having more than 10 markers.

Pelgas et al. BMC Genomics 2011 12:145   doi:10.1186/1471-2164-12-145

Open Data